Starting phenix.real_space_refine on Wed Jun 4 23:05:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ziw_60131/06_2025/8ziw_60131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ziw_60131/06_2025/8ziw_60131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ziw_60131/06_2025/8ziw_60131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ziw_60131/06_2025/8ziw_60131.map" model { file = "/net/cci-nas-00/data/ceres_data/8ziw_60131/06_2025/8ziw_60131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ziw_60131/06_2025/8ziw_60131.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2778 2.51 5 N 711 2.21 5 O 931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4450 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2181 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 261} Chain: "D" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1835 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.58, per 1000 atoms: 0.80 Number of scatterers: 4450 At special positions: 0 Unit cell: (79.872, 96.512, 131.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 931 8.00 N 711 7.00 C 2778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 772 " - pdb=" SG CYS D 896 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 826 " distance=2.03 Simple disulfide: pdb=" SG CYS D 910 " - pdb=" SG CYS D 977 " distance=2.03 Simple disulfide: pdb=" SG CYS D 941 " - pdb=" SG CYS D 956 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA B 3 " - " MAN B 4 " " BMA H 3 " - " MAN H 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " BETA1-6 " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG B 1 " - " ASN A 534 " " NAG C 1 " - " ASN A 630 " " NAG E 1 " - " ASN A 682 " " NAG F 1 " - " ASN A 706 " " NAG G 1 " - " ASN A 725 " " NAG H 1 " - " ASN D 848 " " NAG I 1 " - " ASN D 887 " " NAG J 1 " - " ASN D 909 " " NAG K 1 " - " ASN D 949 " " NAG L 1 " - " ASN D 980 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 510.1 milliseconds 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 6.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'D' and resid 833 through 835 No H-bonds generated for 'chain 'D' and resid 833 through 835' Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.579A pdb=" N GLN D 943 " --> pdb=" O GLU D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 952 No H-bonds generated for 'chain 'D' and resid 950 through 952' Processing helix chain 'D' and resid 1010 through 1017 removed outlier: 4.133A pdb=" N PHE D1017 " --> pdb=" O TRP D1013 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 538 removed outlier: 4.161A pdb=" N PHE A 537 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA A 629 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A 570 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ASN A 630 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE A 568 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 552 through 557 removed outlier: 3.608A pdb=" N CYS A 552 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 648 through 649 Processing sheet with id=AA4, first strand: chain 'A' and resid 679 through 681 removed outlier: 3.629A pdb=" N ARG A 692 " --> pdb=" O ARG A 679 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 679 through 681 removed outlier: 3.629A pdb=" N ARG A 692 " --> pdb=" O ARG A 679 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 739 through 742 removed outlier: 3.805A pdb=" N ASN A 742 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE A 750 " --> pdb=" O ASN A 742 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 789 through 790 removed outlier: 4.121A pdb=" N CYS D 956 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 957 " --> pdb=" O GLY D1002 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D1002 " --> pdb=" O ALA D 957 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL D1003 " --> pdb=" O SER D 990 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 988 " --> pdb=" O ALA D1005 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU D 985 " --> pdb=" O CYS D 977 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS D 977 " --> pdb=" O LEU D 985 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA D 913 " --> pdb=" O PRO D 974 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 799 through 804 removed outlier: 3.862A pdb=" N CYS D 810 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR D 804 " --> pdb=" O LEU D 808 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU D 808 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 855 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N TRP D 837 " --> pdb=" O ILE D 859 " (cutoff:3.500A) 81 hydrogen bonds defined for protein. 222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1382 1.34 - 1.46: 1098 1.46 - 1.58: 2037 1.58 - 1.70: 0 1.70 - 1.81: 37 Bond restraints: 4554 Sorted by residual: bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.76e+00 bond pdb=" C5 MAN H 4 " pdb=" O5 MAN H 4 " ideal model delta sigma weight residual 1.418 1.460 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 MAN I 4 " pdb=" C2 MAN I 4 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.399 1.437 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C GLU A 532 " pdb=" N PRO A 533 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.42e+00 ... (remaining 4549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 5838 1.37 - 2.74: 238 2.74 - 4.11: 65 4.11 - 5.48: 51 5.48 - 6.85: 18 Bond angle restraints: 6210 Sorted by residual: angle pdb=" N ARG D 982 " pdb=" CA ARG D 982 " pdb=" C ARG D 982 " ideal model delta sigma weight residual 114.56 110.45 4.11 1.27e+00 6.20e-01 1.05e+01 angle pdb=" N LEU D 849 " pdb=" CA LEU D 849 " pdb=" C LEU D 849 " ideal model delta sigma weight residual 113.43 110.25 3.18 1.26e+00 6.30e-01 6.37e+00 angle pdb=" C THR A 522 " pdb=" CA THR A 522 " pdb=" CB THR A 522 " ideal model delta sigma weight residual 110.42 115.41 -4.99 1.99e+00 2.53e-01 6.30e+00 angle pdb=" CA ARG D 982 " pdb=" C ARG D 982 " pdb=" N TRP D 983 " ideal model delta sigma weight residual 119.26 116.48 2.78 1.14e+00 7.69e-01 5.96e+00 angle pdb=" C3 NAG I 2 " pdb=" C4 NAG I 2 " pdb=" O4 NAG I 2 " ideal model delta sigma weight residual 107.29 114.14 -6.85 3.00e+00 1.11e-01 5.21e+00 ... (remaining 6205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 2951 23.74 - 47.48: 63 47.48 - 71.22: 30 71.22 - 94.96: 55 94.96 - 118.70: 41 Dihedral angle restraints: 3140 sinusoidal: 1660 harmonic: 1480 Sorted by residual: dihedral pdb=" CB CYS A 772 " pdb=" SG CYS A 772 " pdb=" SG CYS D 896 " pdb=" CB CYS D 896 " ideal model delta sinusoidal sigma weight residual -86.00 -123.99 37.99 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" C2 MAN H 4 " pdb=" C1 MAN H 4 " pdb=" O5 MAN H 4 " pdb=" C5 MAN H 4 " ideal model delta sinusoidal sigma weight residual -57.62 61.08 -118.70 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.29 110.42 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 3137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 676 0.080 - 0.160: 92 0.160 - 0.240: 2 0.240 - 0.319: 11 0.319 - 0.399: 2 Chirality restraints: 783 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN D 909 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 534 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 780 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 731 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 732 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 732 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 732 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 542 " -0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 543 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 973 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO D 974 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 974 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 974 " -0.015 5.00e-02 4.00e+02 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 818 2.78 - 3.31: 4012 3.31 - 3.84: 6956 3.84 - 4.37: 7702 4.37 - 4.90: 13175 Nonbonded interactions: 32663 Sorted by model distance: nonbonded pdb=" O3 NAG I 2 " pdb=" O6 MAN I 4 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASN D 875 " pdb=" ND2 ASN D 953 " model vdw 2.263 3.120 nonbonded pdb=" NE1 TRP A 707 " pdb=" OG SER A 712 " model vdw 2.336 3.120 nonbonded pdb=" OD1 ASP D 874 " pdb=" ND2 ASN D 953 " model vdw 2.342 3.120 nonbonded pdb=" O TRP D1013 " pdb=" OG SER D1016 " model vdw 2.362 3.040 ... (remaining 32658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.650 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4593 Z= 0.243 Angle : 0.883 9.468 6322 Z= 0.351 Chirality : 0.060 0.399 783 Planarity : 0.003 0.030 766 Dihedral : 22.014 118.698 2177 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.81 % Allowed : 3.84 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.38), residues: 515 helix: 0.01 (0.95), residues: 35 sheet: 1.00 (0.51), residues: 113 loop : -1.19 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 554 HIS 0.003 0.000 HIS D1019 PHE 0.004 0.001 PHE A 693 TYR 0.005 0.001 TYR A 546 ARG 0.001 0.000 ARG D1009 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 10) link_NAG-ASN : angle 2.31909 ( 30) link_ALPHA1-6 : bond 0.00820 ( 2) link_ALPHA1-6 : angle 1.77729 ( 6) link_BETA1-4 : bond 0.00563 ( 18) link_BETA1-4 : angle 3.10784 ( 54) link_ALPHA1-3 : bond 0.00668 ( 2) link_ALPHA1-3 : angle 1.40351 ( 6) hydrogen bonds : bond 0.27402 ( 78) hydrogen bonds : angle 11.62711 ( 222) link_BETA1-6 : bond 0.00654 ( 2) link_BETA1-6 : angle 1.41513 ( 6) SS BOND : bond 0.00108 ( 5) SS BOND : angle 0.39626 ( 10) covalent geometry : bond 0.00476 ( 4554) covalent geometry : angle 0.82232 ( 6210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 LEU cc_start: 0.8380 (mt) cc_final: 0.8161 (mp) outliers start: 8 outliers final: 2 residues processed: 81 average time/residue: 0.7742 time to fit residues: 66.3695 Evaluate side-chains 73 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 853 GLN D 881 HIS ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 968 GLN ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.204239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.189983 restraints weight = 8141.898| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 3.32 r_work: 0.4358 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4593 Z= 0.175 Angle : 0.929 9.412 6322 Z= 0.389 Chirality : 0.055 0.335 783 Planarity : 0.005 0.043 766 Dihedral : 17.943 100.585 1242 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.71 % Allowed : 9.48 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.37), residues: 515 helix: -0.70 (0.87), residues: 34 sheet: 0.36 (0.49), residues: 123 loop : -1.29 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 699 HIS 0.006 0.002 HIS D 881 PHE 0.016 0.002 PHE D1010 TYR 0.017 0.002 TYR D 948 ARG 0.005 0.001 ARG A 624 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 10) link_NAG-ASN : angle 2.59978 ( 30) link_ALPHA1-6 : bond 0.00942 ( 2) link_ALPHA1-6 : angle 2.94005 ( 6) link_BETA1-4 : bond 0.00553 ( 18) link_BETA1-4 : angle 3.79572 ( 54) link_ALPHA1-3 : bond 0.00893 ( 2) link_ALPHA1-3 : angle 2.40375 ( 6) hydrogen bonds : bond 0.04149 ( 78) hydrogen bonds : angle 8.60939 ( 222) link_BETA1-6 : bond 0.00705 ( 2) link_BETA1-6 : angle 2.95101 ( 6) SS BOND : bond 0.00498 ( 5) SS BOND : angle 0.67329 ( 10) covalent geometry : bond 0.00353 ( 4554) covalent geometry : angle 0.83531 ( 6210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 880 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6457 (mtp) outliers start: 12 outliers final: 7 residues processed: 75 average time/residue: 0.8697 time to fit residues: 68.6431 Evaluate side-chains 75 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.203093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.188682 restraints weight = 8022.976| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 3.35 r_work: 0.4347 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4593 Z= 0.161 Angle : 0.890 9.153 6322 Z= 0.370 Chirality : 0.055 0.297 783 Planarity : 0.004 0.035 766 Dihedral : 14.474 94.035 1241 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.93 % Allowed : 11.74 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.36), residues: 515 helix: -1.57 (0.80), residues: 33 sheet: 0.09 (0.47), residues: 122 loop : -1.48 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 554 HIS 0.006 0.002 HIS A 700 PHE 0.013 0.002 PHE D1010 TYR 0.016 0.002 TYR D 948 ARG 0.007 0.001 ARG A 624 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 10) link_NAG-ASN : angle 2.41661 ( 30) link_ALPHA1-6 : bond 0.01114 ( 2) link_ALPHA1-6 : angle 3.13910 ( 6) link_BETA1-4 : bond 0.00569 ( 18) link_BETA1-4 : angle 3.62748 ( 54) link_ALPHA1-3 : bond 0.01167 ( 2) link_ALPHA1-3 : angle 1.66101 ( 6) hydrogen bonds : bond 0.03995 ( 78) hydrogen bonds : angle 7.91771 ( 222) link_BETA1-6 : bond 0.00561 ( 2) link_BETA1-6 : angle 2.37852 ( 6) SS BOND : bond 0.00436 ( 5) SS BOND : angle 0.43088 ( 10) covalent geometry : bond 0.00333 ( 4554) covalent geometry : angle 0.80397 ( 6210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.7660 (tt0) cc_final: 0.7436 (tt0) REVERT: D 880 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.6282 (mtp) outliers start: 13 outliers final: 6 residues processed: 82 average time/residue: 0.8880 time to fit residues: 76.5695 Evaluate side-chains 81 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Chi-restraints excluded: chain D residue 999 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.202745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.188706 restraints weight = 8039.720| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 3.17 r_work: 0.4339 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4593 Z= 0.156 Angle : 0.880 9.592 6322 Z= 0.366 Chirality : 0.055 0.320 783 Planarity : 0.005 0.062 766 Dihedral : 12.708 90.970 1241 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 2.71 % Allowed : 13.54 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.36), residues: 515 helix: -1.39 (0.77), residues: 34 sheet: -0.10 (0.47), residues: 122 loop : -1.53 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 554 HIS 0.005 0.001 HIS D1019 PHE 0.019 0.001 PHE A 551 TYR 0.014 0.002 TYR D 948 ARG 0.002 0.000 ARG D 908 Details of bonding type rmsd link_NAG-ASN : bond 0.00633 ( 10) link_NAG-ASN : angle 2.57298 ( 30) link_ALPHA1-6 : bond 0.01207 ( 2) link_ALPHA1-6 : angle 3.20460 ( 6) link_BETA1-4 : bond 0.00565 ( 18) link_BETA1-4 : angle 3.57233 ( 54) link_ALPHA1-3 : bond 0.01210 ( 2) link_ALPHA1-3 : angle 1.82987 ( 6) hydrogen bonds : bond 0.03425 ( 78) hydrogen bonds : angle 7.58842 ( 222) link_BETA1-6 : bond 0.00579 ( 2) link_BETA1-6 : angle 2.37307 ( 6) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.67351 ( 10) covalent geometry : bond 0.00318 ( 4554) covalent geometry : angle 0.79162 ( 6210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7501 (ptp90) REVERT: D 880 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.6209 (mtp) outliers start: 12 outliers final: 7 residues processed: 82 average time/residue: 1.0443 time to fit residues: 91.3100 Evaluate side-chains 82 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Chi-restraints excluded: chain D residue 999 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.0060 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.203243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.189198 restraints weight = 8168.884| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 3.19 r_work: 0.4340 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4593 Z= 0.146 Angle : 0.855 9.319 6322 Z= 0.359 Chirality : 0.053 0.304 783 Planarity : 0.005 0.058 766 Dihedral : 11.518 84.958 1241 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 2.26 % Allowed : 14.22 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.36), residues: 515 helix: -1.36 (0.77), residues: 34 sheet: -0.21 (0.46), residues: 122 loop : -1.58 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 915 HIS 0.006 0.001 HIS D1019 PHE 0.024 0.002 PHE A 551 TYR 0.012 0.001 TYR D 948 ARG 0.007 0.001 ARG D 908 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 10) link_NAG-ASN : angle 2.47386 ( 30) link_ALPHA1-6 : bond 0.01282 ( 2) link_ALPHA1-6 : angle 3.25138 ( 6) link_BETA1-4 : bond 0.00577 ( 18) link_BETA1-4 : angle 3.44421 ( 54) link_ALPHA1-3 : bond 0.01270 ( 2) link_ALPHA1-3 : angle 1.74419 ( 6) hydrogen bonds : bond 0.03173 ( 78) hydrogen bonds : angle 7.34864 ( 222) link_BETA1-6 : bond 0.00615 ( 2) link_BETA1-6 : angle 2.02183 ( 6) SS BOND : bond 0.00278 ( 5) SS BOND : angle 0.52306 ( 10) covalent geometry : bond 0.00298 ( 4554) covalent geometry : angle 0.77070 ( 6210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.7757 (mtt180) cc_final: 0.7519 (ptp90) REVERT: D 879 MET cc_start: 0.7345 (mmm) cc_final: 0.7000 (mmm) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.7791 time to fit residues: 66.8035 Evaluate side-chains 83 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Chi-restraints excluded: chain D residue 999 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.202998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.188285 restraints weight = 8002.337| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 3.38 r_work: 0.4324 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4593 Z= 0.149 Angle : 0.858 9.322 6322 Z= 0.361 Chirality : 0.052 0.298 783 Planarity : 0.005 0.053 766 Dihedral : 11.214 76.488 1241 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 3.39 % Allowed : 12.87 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.35), residues: 515 helix: -1.30 (0.77), residues: 34 sheet: -0.17 (0.47), residues: 112 loop : -1.63 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 915 HIS 0.006 0.001 HIS D1019 PHE 0.020 0.001 PHE A 551 TYR 0.012 0.001 TYR D 948 ARG 0.007 0.001 ARG D 908 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 10) link_NAG-ASN : angle 2.50000 ( 30) link_ALPHA1-6 : bond 0.01342 ( 2) link_ALPHA1-6 : angle 3.24565 ( 6) link_BETA1-4 : bond 0.00590 ( 18) link_BETA1-4 : angle 3.41385 ( 54) link_ALPHA1-3 : bond 0.01241 ( 2) link_ALPHA1-3 : angle 1.65406 ( 6) hydrogen bonds : bond 0.03000 ( 78) hydrogen bonds : angle 7.30302 ( 222) link_BETA1-6 : bond 0.00606 ( 2) link_BETA1-6 : angle 1.95772 ( 6) SS BOND : bond 0.00324 ( 5) SS BOND : angle 0.57898 ( 10) covalent geometry : bond 0.00306 ( 4554) covalent geometry : angle 0.77464 ( 6210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7545 (ptp90) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 1.1789 time to fit residues: 101.7094 Evaluate side-chains 86 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 694 ARG Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Chi-restraints excluded: chain D residue 999 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 902 GLN ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.200501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.186259 restraints weight = 7954.606| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 3.16 r_work: 0.4302 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4593 Z= 0.180 Angle : 0.912 10.357 6322 Z= 0.385 Chirality : 0.055 0.311 783 Planarity : 0.006 0.057 766 Dihedral : 11.142 59.685 1241 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 3.16 % Allowed : 14.00 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.35), residues: 515 helix: -1.41 (0.76), residues: 34 sheet: -0.24 (0.48), residues: 112 loop : -1.82 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 915 HIS 0.006 0.001 HIS D1019 PHE 0.020 0.002 PHE A 551 TYR 0.013 0.002 TYR D 959 ARG 0.006 0.001 ARG D 908 Details of bonding type rmsd link_NAG-ASN : bond 0.00757 ( 10) link_NAG-ASN : angle 2.81334 ( 30) link_ALPHA1-6 : bond 0.01446 ( 2) link_ALPHA1-6 : angle 3.10400 ( 6) link_BETA1-4 : bond 0.00696 ( 18) link_BETA1-4 : angle 3.63393 ( 54) link_ALPHA1-3 : bond 0.01274 ( 2) link_ALPHA1-3 : angle 1.50220 ( 6) hydrogen bonds : bond 0.03164 ( 78) hydrogen bonds : angle 7.24990 ( 222) link_BETA1-6 : bond 0.00562 ( 2) link_BETA1-6 : angle 2.14549 ( 6) SS BOND : bond 0.00353 ( 5) SS BOND : angle 0.79421 ( 10) covalent geometry : bond 0.00364 ( 4554) covalent geometry : angle 0.82220 ( 6210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 ASN cc_start: 0.6421 (t0) cc_final: 0.6198 (t0) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 0.6674 time to fit residues: 61.1028 Evaluate side-chains 87 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Chi-restraints excluded: chain D residue 999 ASN Chi-restraints excluded: chain D residue 1003 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.202522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.187912 restraints weight = 7837.864| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 3.33 r_work: 0.4315 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4593 Z= 0.147 Angle : 0.877 9.283 6322 Z= 0.374 Chirality : 0.052 0.299 783 Planarity : 0.006 0.074 766 Dihedral : 10.447 58.939 1241 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 2.93 % Allowed : 14.67 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.36), residues: 515 helix: -1.60 (0.75), residues: 33 sheet: -0.30 (0.49), residues: 112 loop : -1.76 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 915 HIS 0.006 0.001 HIS D1019 PHE 0.017 0.002 PHE A 551 TYR 0.029 0.002 TYR D 948 ARG 0.009 0.001 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 10) link_NAG-ASN : angle 2.53208 ( 30) link_ALPHA1-6 : bond 0.01458 ( 2) link_ALPHA1-6 : angle 2.79665 ( 6) link_BETA1-4 : bond 0.00623 ( 18) link_BETA1-4 : angle 3.40711 ( 54) link_ALPHA1-3 : bond 0.01189 ( 2) link_ALPHA1-3 : angle 1.52053 ( 6) hydrogen bonds : bond 0.03155 ( 78) hydrogen bonds : angle 7.13017 ( 222) link_BETA1-6 : bond 0.00718 ( 2) link_BETA1-6 : angle 1.83290 ( 6) SS BOND : bond 0.00271 ( 5) SS BOND : angle 0.71753 ( 10) covalent geometry : bond 0.00307 ( 4554) covalent geometry : angle 0.79788 ( 6210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8197 (tm-30) REVERT: A 742 ASN cc_start: 0.6426 (t0) cc_final: 0.6176 (t0) outliers start: 13 outliers final: 12 residues processed: 82 average time/residue: 0.7544 time to fit residues: 65.7480 Evaluate side-chains 85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 944 GLN Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Chi-restraints excluded: chain D residue 999 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 19 optimal weight: 0.0770 chunk 34 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.0170 chunk 22 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.204018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.189562 restraints weight = 7902.869| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 3.34 r_work: 0.4334 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4593 Z= 0.125 Angle : 0.829 9.316 6322 Z= 0.352 Chirality : 0.050 0.304 783 Planarity : 0.006 0.080 766 Dihedral : 9.878 59.301 1241 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.48 % Allowed : 15.35 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.36), residues: 515 helix: -1.66 (0.74), residues: 33 sheet: -0.17 (0.50), residues: 98 loop : -1.69 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 699 HIS 0.006 0.001 HIS D1019 PHE 0.024 0.002 PHE A 551 TYR 0.018 0.001 TYR D 948 ARG 0.016 0.001 ARG A 692 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 10) link_NAG-ASN : angle 2.36411 ( 30) link_ALPHA1-6 : bond 0.01334 ( 2) link_ALPHA1-6 : angle 2.40558 ( 6) link_BETA1-4 : bond 0.00613 ( 18) link_BETA1-4 : angle 3.20892 ( 54) link_ALPHA1-3 : bond 0.01107 ( 2) link_ALPHA1-3 : angle 1.46611 ( 6) hydrogen bonds : bond 0.03113 ( 78) hydrogen bonds : angle 6.88670 ( 222) link_BETA1-6 : bond 0.00733 ( 2) link_BETA1-6 : angle 1.64475 ( 6) SS BOND : bond 0.00338 ( 5) SS BOND : angle 0.77113 ( 10) covalent geometry : bond 0.00262 ( 4554) covalent geometry : angle 0.75658 ( 6210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 ASN cc_start: 0.6390 (t0) cc_final: 0.6148 (t0) REVERT: D 879 MET cc_start: 0.7494 (mmm) cc_final: 0.7095 (mmm) outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 0.7145 time to fit residues: 53.9520 Evaluate side-chains 74 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 944 GLN Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Chi-restraints excluded: chain D residue 999 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 0.0470 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.0030 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 overall best weight: 0.3866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.203802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.189821 restraints weight = 7876.881| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 3.17 r_work: 0.4341 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4593 Z= 0.131 Angle : 0.840 9.287 6322 Z= 0.358 Chirality : 0.051 0.298 783 Planarity : 0.006 0.064 766 Dihedral : 9.854 59.022 1241 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 2.26 % Allowed : 16.25 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.36), residues: 515 helix: -1.63 (0.74), residues: 33 sheet: -0.51 (0.48), residues: 107 loop : -1.67 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 554 HIS 0.005 0.001 HIS D1019 PHE 0.027 0.002 PHE A 551 TYR 0.020 0.001 TYR D 948 ARG 0.013 0.001 ARG A 692 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 10) link_NAG-ASN : angle 2.41674 ( 30) link_ALPHA1-6 : bond 0.01240 ( 2) link_ALPHA1-6 : angle 2.27530 ( 6) link_BETA1-4 : bond 0.00603 ( 18) link_BETA1-4 : angle 3.19405 ( 54) link_ALPHA1-3 : bond 0.01069 ( 2) link_ALPHA1-3 : angle 1.36608 ( 6) hydrogen bonds : bond 0.03019 ( 78) hydrogen bonds : angle 6.83054 ( 222) link_BETA1-6 : bond 0.00697 ( 2) link_BETA1-6 : angle 1.69632 ( 6) SS BOND : bond 0.00295 ( 5) SS BOND : angle 0.75072 ( 10) covalent geometry : bond 0.00278 ( 4554) covalent geometry : angle 0.76901 ( 6210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 ASN cc_start: 0.6374 (t0) cc_final: 0.6128 (t0) REVERT: D 879 MET cc_start: 0.7397 (mmm) cc_final: 0.6987 (mmm) REVERT: D 1004 TYR cc_start: 0.7680 (m-80) cc_final: 0.7361 (m-10) outliers start: 10 outliers final: 9 residues processed: 72 average time/residue: 0.7737 time to fit residues: 59.2204 Evaluate side-chains 73 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 944 GLN Chi-restraints excluded: chain D residue 980 ASN Chi-restraints excluded: chain D residue 999 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 37 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.202147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.188286 restraints weight = 7843.471| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 3.13 r_work: 0.4325 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4593 Z= 0.150 Angle : 0.863 9.238 6322 Z= 0.368 Chirality : 0.052 0.288 783 Planarity : 0.006 0.065 766 Dihedral : 10.034 59.363 1241 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 2.26 % Allowed : 16.03 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.36), residues: 515 helix: -1.67 (0.74), residues: 33 sheet: -0.46 (0.50), residues: 107 loop : -1.72 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 983 HIS 0.005 0.001 HIS D1019 PHE 0.029 0.002 PHE A 551 TYR 0.021 0.002 TYR D 948 ARG 0.011 0.001 ARG A 692 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 10) link_NAG-ASN : angle 2.58864 ( 30) link_ALPHA1-6 : bond 0.01143 ( 2) link_ALPHA1-6 : angle 2.21189 ( 6) link_BETA1-4 : bond 0.00640 ( 18) link_BETA1-4 : angle 3.31751 ( 54) link_ALPHA1-3 : bond 0.01100 ( 2) link_ALPHA1-3 : angle 1.31098 ( 6) hydrogen bonds : bond 0.03019 ( 78) hydrogen bonds : angle 6.98739 ( 222) link_BETA1-6 : bond 0.00615 ( 2) link_BETA1-6 : angle 1.95306 ( 6) SS BOND : bond 0.00373 ( 5) SS BOND : angle 0.68567 ( 10) covalent geometry : bond 0.00310 ( 4554) covalent geometry : angle 0.78656 ( 6210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.10 seconds wall clock time: 70 minutes 2.06 seconds (4202.06 seconds total)